Other primer properties

The forward and reverse primers should have similar biochemical properties to ensure a balanced PCR reaction. If several PCR reactions are carried out

Prim erBank

- PCR Primers For Gene Expression Detection or Quantification

Primer Search Help I FAQ PCR Protocol Priroer Statistics Comments Links

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Figure 5.2

A screenshot of the web interface for PrimerBank. There are several ways to search for primers: GenBank Accession, NCBI protein accession, Gene ID, PrimerBank ID or Keyword. PrimerBank currently contains over 300,000 primers designed for most known human and mouse genes.

simultaneously, it is important that all primers in the reactions be similar.

To provide flexibility in PCR setup, all of our in silico designed primers have similar properties.

• The primer length is 18-24 residues

• 3' end stability. The AG value for the five 3' end bases is at least 9 kcal/mol.

• The PCR product length is 100-250 bp. Occasionally if this requirement cannot be satisfied, alternative length ranges are used.

• No primer is designed from low-complexity regions. The low-complexity regions are identified and excluded from primer design by the NCBI DUST program (Hancock and Armstrong, 1994).

• A primer does not contain 6 or more contiguous same nucleotides.

• A primer does not contain any ambiguous nucleotide.

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